| sub6 |
| ID: | 1404139133 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (157) | ||
| Sequences: | 672 (271) | ||
| Seq/Len: | 4.280 | ||
| Nf(neff/√len): | 21.6 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 4.280).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 96_W | 105_V | 3.811 | 1.00 |
| 61_A | 66_E | 3.663 | 1.00 |
| 107_S | 113_S | 2.955 | 1.00 |
| 33_S | 159_R | 2.571 | 1.00 |
| 42_G | 47_A | 2.316 | 1.00 |
| 93_R | 97_E | 2.125 | 1.00 |
| 65_S | 155_Q | 1.861 | 1.00 |
| 36_L | 158_V | 1.769 | 1.00 |
| 104_W | 125_Q | 1.724 | 0.99 |
| 39_A | 95_V | 1.707 | 0.99 |
| 117_M | 125_Q | 1.670 | 0.99 |
| 105_V | 133_V | 1.662 | 0.99 |
| 153_Q | 156_K | 1.638 | 0.99 |
| 149_Y | 153_Q | 1.635 | 0.99 |
| 85_S | 120_N | 1.594 | 0.99 |
| 85_S | 123_I | 1.577 | 0.99 |
| 79_I | 147_L | 1.573 | 0.99 |
| 43_L | 50_M | 1.568 | 0.99 |
| 93_R | 131_V | 1.564 | 0.99 |
| 89_A | 130_V | 1.558 | 0.98 |
| 91_V | 125_Q | 1.548 | 0.98 |
| 91_V | 120_N | 1.501 | 0.98 |
| 61_A | 67_V | 1.484 | 0.98 |
| 110_A | 113_S | 1.472 | 0.98 |
| 83_R | 123_I | 1.457 | 0.97 |
| 21_F | 77_V | 1.456 | 0.97 |
| 43_L | 84_L | 1.440 | 0.97 |
| 118_F | 138_P | 1.432 | 0.97 |
| 50_M | 68_F | 1.431 | 0.97 |
| 40_T | 68_F | 1.415 | 0.97 |
| 108_M | 147_L | 1.405 | 0.96 |
| 84_L | 92_M | 1.404 | 0.96 |
| 40_T | 70_A | 1.371 | 0.96 |
| 39_A | 81_A | 1.343 | 0.95 |
| 27_L | 77_V | 1.333 | 0.95 |
| 46_C | 141_P | 1.321 | 0.95 |
| 79_I | 108_M | 1.304 | 0.94 |
| 50_M | 147_L | 1.283 | 0.93 |
| 36_L | 77_V | 1.279 | 0.93 |
| 84_L | 127_V | 1.274 | 0.93 |
| 42_G | 81_A | 1.269 | 0.93 |
| 137_V | 150_A | 1.267 | 0.93 |
| 60_L | 148_I | 1.254 | 0.92 |
| 117_M | 120_N | 1.218 | 0.91 |
| 31_G | 34_N | 1.205 | 0.90 |
| 61_A | 68_F | 1.203 | 0.90 |
| 32_R | 76_D | 1.191 | 0.90 |
| 44_A | 83_R | 1.164 | 0.88 |
| 126_N | 136_Y | 1.156 | 0.88 |
| 77_V | 154_L | 1.154 | 0.87 |
| 29_A | 32_R | 1.154 | 0.87 |
| 110_A | 150_A | 1.154 | 0.87 |
| 95_V | 113_S | 1.131 | 0.86 |
| 81_A | 108_M | 1.120 | 0.85 |
| 43_L | 47_A | 1.118 | 0.85 |
| 24_L | 28_V | 1.115 | 0.85 |
| 121_Y | 133_V | 1.113 | 0.85 |
| 40_T | 114_S | 1.110 | 0.85 |
| 70_A | 75_A | 1.103 | 0.84 |
| 48_I | 52_A | 1.086 | 0.83 |
| 83_R | 120_N | 1.084 | 0.83 |
| 74_Q | 98_Q | 1.060 | 0.81 |
| 117_M | 144_P | 1.051 | 0.80 |
| 23_T | 26_K | 1.050 | 0.80 |
| 22_T | 77_V | 1.048 | 0.80 |
| 44_A | 51_M | 1.043 | 0.79 |
| 89_A | 93_R | 1.042 | 0.79 |
| 44_A | 47_A | 1.042 | 0.79 |
| 52_A | 143_R | 1.037 | 0.79 |
| 52_A | 84_L | 1.037 | 0.79 |
| 86_K | 117_M | 1.033 | 0.78 |
| 65_S | 77_V | 1.023 | 0.77 |
| 40_T | 50_M | 1.019 | 0.77 |
| 84_L | 113_S | 1.016 | 0.77 |
| 96_W | 118_F | 1.011 | 0.76 |
| 47_A | 51_M | 1.004 | 0.75 |
| 118_F | 123_I | 1.002 | 0.75 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3i9v6 | 2 | 0.8011 | 100 | 0.212 | Contact Map |
| 1yq9A | 2 | 0.8343 | 100 | 0.575 | Contact Map |
| 1h2aS | 1 | 0.8453 | 100 | 0.584 | Contact Map |
| 3ze9A | 1 | 0.8122 | 100 | 0.597 | Contact Map |
| 1wuiS | 1 | 0.8453 | 100 | 0.599 | Contact Map |
| 3uqyS | 2 | 0.8287 | 100 | 0.601 | Contact Map |
| 3myrA | 4 | 0.8343 | 100 | 0.603 | Contact Map |
| 3ayxB | 2 | 0.8287 | 100 | 0.604 | Contact Map |
| 1yqwA | 3 | 0.8232 | 100 | 0.604 | Contact Map |
| 4iucS | 1 | 0.8287 | 100 | 0.605 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)